Are sponges the closest relatives of the rest of the animals?

March 21, 2021 • 9:30 am

A new paper in Nature Communications highlights an ongoing controversy in the evolution of animals: what are the closest relatives of living multicellular animals?

First, though, we need to refresh ourselves on what “animals” are. Merriam-Webster defines them adequately:

Any of a kingdom (Animalia) of living things including many-celled organisms and often many of the single-celled ones(such as protozoans) that typically differ from plants in having cells without cellulose walls, in lacking chlorophyll and the capacity for photosynthesis, in requiring more complex food materials (such as proteins), in being organized to a greater degree of complexity, and in having the capacity for spontaneous movement and rapid motor responses to stimulation.

We’re leaving out the single-celled “animals” here (under “outgroups” in the figure below) and concentrating on multicellular animals.

The multicellular animals include (as the phylogenies show below), Ctenophores, or comb jellies, Porifera (sponges), Placozoans (free living but small multicellular organisms), Cnidaria (corals, jellyfish, sea anemones and their relatives), and Bilateria (everything else; all animals with a head and tail end, as well as a belly and a back at some stage of their life, including echinoderms which have these features as larvae).  Over the years, a combination of developmental, morphological, and molecular analysis has given rise to the two conflicting family trees shown below.

Both trees are the same except for a dispute about the “animal outgroup” (the “breakaway group” or “sister group”), the closest living relative to the vast bulk of the animals, and the first group to branch off from the rest. One school, shown on the left, adheres to the ctenophores, or comb jellies, as this sister group. The other, shown on the right, maintains that sponges occupy this position, and ctenophores branched off later.

 

Here’s an example of a ctenophore (photos from Wikipedia):

And a bunch of sponges:

Now the case for sponges as the sister group is based on the observation that ctenophores share unique features with the other animals, including elements of nervous systems, and (except for Placozoans) muscles and a tubelike digestive system (“gut”). But sponges have none of these. Moreover, sponges are made up of collared cells, or choanocytes, which are similar to “choanoflagellates“, singled-celled protozoans thought to be the closest relative to all the animals from sponges on down. This similarity implies that the common ancestor of multicellular animals might have been something spongelike, supporting the second phylogeny above. That implies that sponges changed relatively little after multicellular animals evolved, while everything else changed a lot more.

But some molecular phylogenies have suggested that the more complex ctenophores might be the outgroup instead of sponges.  This is a bit more problematic to both me and Matthew (see his BBC broadcast below), for if sponges are really more closely related to other animals than are ctenophores, why do ctenophores have muscles, nerves, and an in—>out digestive system like most other animals, but sponges lack these things? To hold that ctenophores are the sister group instead of sponges requires that you posit one of two possibilities:

A.) The common ancestor of all animals had nervous systems and muscles and a gut, which persist in all groups but the sponges, and the sponges lost these features. That seems unlikely, but it’s possible.

or

B.) The common ancestor of all animals lacked these features, but they evolved independently in the choanoflagellates and all other animals save sponges. This seems even more unlikely since it requires the independent evolution of three complex traits in two separate groups (ctenophores and [other animals minus sponges]).

This principle of “parsimony” alone suggests that sponges are the sister group, didn’t lose any of those features, and muscles, nerves, and a gut evolved only once.

The new article in Nature Communications supports the “sponges first” scenario. Click on the screenshot below to read the article, see the pdf here, and find the reference at the bottom of this post. The authors used a new way of making phylogenies using DNA data, dubbed “partition site-heterogeneous models” to eliminate artifacts that may have erroneously shown ctenophores as the sister group of other animals. I’m not going to explain that method and, to be sure, I don’t understand it. In fact, the main results of the paper for the layperson can be described very simply: the new method shows that sponges are the sister group to all animals, a result that makes sense.

I just gave you the punch line, but have to add that the controversy isn’t settled. It is settling, however, as more and more biologists come around to the “sponges split off first” scenario. (I won’t even mention the controversy about the placozoans and ctenophores, and where they fit with relationship to Cnidaria.) Let me just put in the authors’ paragraph where they say that their finding of sponges as the sister group of all other animals is definitive: (my emphasis):

Several studies have already shown that gene family and unpartitioned phylogenomic analyses using more sophisticated substitution models reject Ctenophora sister in favour of Porifera sister. Here, we have consolidated these findings by directly showing that the primary remaining lines of evidence supporting Ctenophora sister, partitioned phylogenomics and measures of underlying support (such as ΔPSlnl values), do not do so when better-fitting site-heterogeneous models are incorporated into the analysis. Thus, the Ctenophora-sister hypothesis can now be wholly rejected in favour of the traditional Porifera-sister scenario of animal evolution, wherein the animal ancestor did not possess key traits such as a nervous system, muscles or a mouth and gut.

Ctenophores as the sister group is now “wholly rejected”! I suspect that not all animal systematists would accept this hypothesis. I do, tentatively, but I don’t fully understand the complex methods of analyzing DNA data (they used 60 animal groups, 406 genes, and 88,384 DNA sites).  My view of these complex methods is the same one that my academic grandfather, Theodosius Dobzhansky, held towards the experts in mathematical population genetics (Dobzhansky was innumerate): “Papa knows best.”

For a fuller explication of the conflict, as well as an overview of animal evolution in general, you can’t do better than Matthew’s 2018 Discovery PROGRAM on the BBC. The controversy about sponges-first versus ctenophores-first starts at 17:45. This program is very good, involves interviews with a lot of different biologists, and should be very clear to the sentient layperson. Plus it’s only half an hour long. Spend this Sunday learning a bit about animal evolution!

Click on the screenshot to hear the show:

_________________

Redmond, A.K., and A. McLysaght 2021. Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding. Nat Commun 12, 1783 (2021). https://doi.org/10.1038/s41467-021-22074-7

Nobel Prize for Physiology or Medicine goes to three for discovering the Hepatitis C virus

October 5, 2020 • 7:00 am

Knowing that the first Nobel Prize for science would be awarded today—in Physiology or Medicine—I made a contest in which readers were to guess just one winner of each of the three science prizes plus the winner of this year’s Literature Nobel.

Well, the first prize was awarded this morning, and the contest is already over. Everyone lost (see here and here).

Granted, this was not an easy one to guess. The award in fact went to three people—Harvey Alter, Michael Houghton, and Charles Rice—with each getting a third of the prize money. The award was given for the discovery of the virus that causes Hepatitis C.  Here’s part of the press release from the Nobel Prize site:

This year’s Nobel Prize is awarded to three scientists who have made a decisive contribution to the fight against blood-borne hepatitis, a major global health problem that causes cirrhosis and liver cancer in people around the world.

Harvey J. Alter, Michael Houghton and Charles M. Rice made seminal discoveries that led to the identification of a novel virus, Hepatitis C virus. Prior to their work, the discovery of the Hepatitis A and B viruses had been critical steps forward, but the majority of blood-borne hepatitis cases remained unexplained. The discovery of Hepatitis C virus revealed the cause of the remaining cases of chronic hepatitis and made possible blood tests and new medicines that have saved millions of lives.

. . . The Nobel Laureates’ discovery of Hepatitis C virus is a landmark achievement in the ongoing battle against viral diseases (Figure 2). Thanks to their discovery, highly sensitive blood tests for the virus are now available and these have essentially eliminated post-transfusion hepatitis in many parts of the world, greatly improving global health. Their discovery also allowed the rapid development of antiviral drugs directed at hepatitis C. For the first time in history, the disease can now be cured, raising hopes of eradicating Hepatitis C virus from the world population. To achieve this goal, international efforts facilitating blood testing and making antiviral drugs available across the globe will be required

Here’s the video of the award with details about the winners, and giving some scientific background; the action starts at 12:50. It’s worth listening to the 20 minutes of science, as you’ll learn a lot. There’s also an interview with the Secretary of the Prize Committee beginning at 34:34.

I guess the prize for CRISPR-Cas9 will have to wait for another year.

Matthew’s theory, which is his, about why Covid-19 and other viral infections often reduce one’s sense of smell

April 1, 2020 • 11:52 am

Matthew tweeted his new theory, which is his, about why Covid-19 patients very often experience “smell blindness”, technically known as anosmia—the loss of one’s sense of smell (which of course also reduces one’s ability to taste). I asked him if he wanted to post it here, and he’s rewritten it so it’s understandable by the science-friendly layperson. And so, without further ado:

A hypothesis to explain why the Covid-19 virus affects the sense of smell in some people

By Matthew Cobb

 

In a recent study by King’s College, London of 579 people who reported having a positive Covid-19 test, 59% said they had reported a loss of smell or taste. This is not unique to Covid-19 – many other viruses can cause the same effect. It has never been quite clear how this occurs. The great amount of attention being paid to Covid-19 has helped reveal one possible mechanism.

We smell volatile molecules, but we don’t directly detect them in the air – our smell neurons would shrivel up and die. Our neurons are protected by a layer of mucus, and the smell molecules have to get through that.

The chemical structure of most smells means they are what is known as hydrophobic – they won’t dissolve easily in water, such as that found in the mucus. It is widely thought that the smells are transported by rather mysterious chaperones called olfactory binding proteins (OBPs).

These molecules are secreted into the mucus by cells called Bowman’s cells in the olfactory epithelium – the layer of skin, high up in the roof of your nasal cavity, which is where you smell things. Many scientists think that OBPs deliver the odour to the receptor on the neuron, and then appear to be taken up by cells called sustentacular cells which lie next door.

A paper that appeared a few days ago suggests that our olfactory neurons don’t express the ACE proteins that are the virus target, and that disruption to our neurons is therefore not the cause of anosmia. However, other cells in the olfactory epithelium, the sustentacular cells and the Bowman’s cells that produce OBPs, do express the ACE protein. Both these cell types are involved in the way that OBPs work.

If the virus is attacking these cells, then the metabolism of OBPs, and thereby the balance of detection of molecules will be altered. This may explain the widespread reports of anosmia following covid-19 infection, and, in some cases like that of the science journalist Adam Rutherford, who had symptoms of covid-19,  hyperosmia (increased sensitivity). Sustentacular cells are also electrically active in newborn mice, perhaps indicating a more complex function for these cell types.

All this suggests that the return of normal olfactory functioning in patients with covid-19, or other coronaviruses, which may also cause these effects, probably depends on the time it takes for the Bowman’s cells and the sustentacular cells to recover.

A simpler explanation – advanced by @stevenmunger on Twitter in response to this – is that infection of these specific cell types merely causes inflammation, which alters tissue function. There may be other hypotheses, too. And some scientists don’t agree that OBPs play much of a role at all in olfaction. “For example, although humans have a number of genes that encode for OBPs, only one kind has so far been identified in the human olfactory epithelium. We clearly need to understand more about this aspect of how we smell.”

Whatever the exact mechanism involved, as Prof Tim Spector of King’s College said: “When combined with other symptoms, people with loss of smell and taste appear to be three times more likely to have contracted Covid-19 according to our data, and should therefore self-isolate for seven days to reduce the spread of the disease.”

For advice on living with anosmia:

fifthsense.org.uk

abscent.org.uk

BBC report of the King’s College study:

https://www.bbc.co.uk/news/health-52111606

References:

Brann et al (2020) – Gene expression in olfactory epithelium, on covid-19 and entry:

Strotmann & Breer (2011) – OBPs and sustentacular cells

Vogalis et al (2005) – Electrical activity in sustentacular cells

Badonnel et al (2009) – OBPs secreted by Bowman’s cells

 

A prediction: Do blind people dream?

December 24, 2018 • 6:30 pm

 

CLARIFICATION; By “dreaming” here, I was asking whether blind people have visual dreams.

The NBC News tonight broadcast a segment about a little girl who was born blind but has a really positive attitude: she has her own upbeat show on local radio, reading from a Braille script, and says that the only thing she can’t do is “see.”

That instantly got me wondering: Do blind people dream?  And here’s a prediction—actually three predictions—before I’ve checked on the Internet. (I don’t think I’ll check until tomorrow, or I’ll wait until a reader tells me.)

The first prediction, which is mine, is based on the supposition that if someone is born blind, they’ve never been able to process visual input and therefore couldn’t experience it in their brain. Therefore, I predict that they would not be able to dream.

But people who go blind after they’re born would have developed the brain ability and experience of seeing and would have the neural ability to dream. BUT—the third prediction—the longer they’ve been blind, the less reinforcement of their brain-eye connection they’d have, and I predict that they’d gradually lose the ability to dream, or at least the frequency of dreaming would wane.

It’s strange that I’ve never thought about this before.